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What are the 3 basic structural components of amino acids?

-An amino group (-NH2)
-A carboxyl group (-COOH)
-A side chain (R)

Primary structure of amino acids:

sequence of amino acids in a polypeptide chain; linked with strong covalent peptide bonds

The specific sequence of amino acids...

-differentiates proteins
-dictates secondary & tertiary structures
-determines ultimate function

Secondary structure of proteins:

weak repeating linkages between nearby amino acids (ie H-bonds); promotes strength and rigidity, necessary in structural proteins

Types of secondary structure:

- alpha-helix: coiling of polypeptide chain forming a cylindrical shape
- beta-pleated sheet: accordion-like
- random coil: less stable due to amino acid side chain interference

Tertiary structure:

results from folding of a protein back upon itself, allowing interactions/bonds between R-groups on amino acids that are distant in the primary chain

Types of interactions in tertiary structure:

-hydrogen bonds
-hydrophobic amino acids cluster in center
-electrostatic attraction of oppositely charged aas
-disulfide bridges (strong covalent bonds) between cysteine residues

Disulfide bond

(aka disulfide bridge) is a covalent bond formed thru oxidation of 2 thiol or sulfhydryl groups (R-SH); is one of the mechanisms by which tertiary structure is maintained (ex. cystine-cystine)

Protein classifications based on tertiary structure:

-Globular proteins
-Fibrous proteins
-membrane proteins

Globular proteins

generally soluble; includes most enzymes

Fibrous proteins

generally structural (ex collagen, keratin, elastin

Membrane proteins

generally receptors or channels that facilitate or control transport of molecules through membranes

Quarternary structure

results from association of several "subunit" polypeptide chains, linked by hydrogen or electrostatic bonding to form an oligomer

Conformational change in quarternary structure

conformational change in one subunit may affect structure and function of other subunits (ex hemoglobin)

Native conformation

is the conformation in which a molecule is biologically active


proteins that assist the non-covalent folding or unfolding and the assembly or disassembly of other macromeloecular structures, but do not occur in these structures when the structures are performing their normal biological functions

Folding of proteins

occurs during synthesis, aided by chaperones

Can denatured proteins regain native conformation?

Denatured proteins do not spontaneously regain native conformation.

Amino Acid Polarity:

tendency to interact with water; non-polar amino acids are hydrophobic

AA Electrical charge:

based on ionization at physiological pH


have no charge in R group, so amino (+) and carboxy (-) group charges cancel each other and result in no net charge.

AA classification by

-electric charge
-structure (of side chain)

Side chains that are electrically charged or contain hydroxyl groups are __________ and interact with water, so tend to orient ____________ part of the protein.

tend to project on the surface of proteins

Side chains with phenyl rings are _________, hydrophobic, and often orient ___________ of protein structures.

orient toward the inside of protein structures

Acidic side chains ___________ hydrogens.

release hydrogens

Basic side chains __________ hydrogens.

accept hydrogens

AA can act as a buffering system in blood by

AA in proteins accept hydrogens when pH is too low, and donate hydrogens when the pH is too high.

Aliphatic AA side chains

contain hydrogen or hydrogen and carbon in straight chain or branched configuration (non-cyclic/non-aromatic)

Sulfur containing AA are
polar or nonpolar; hydro- phobic or philic?


Post-translationally & biosynthetically formed sulfur containing aa

slide 28

Essential (indispensable) amino acids:

AA's that cannot by synthesized in the body and must be present in the diet.

Totally indispensable amino acids:

cannot be synthesized sufficiently from their alph-keto acids

What are the totally indispensable aa's?

Threonine, Histidine, Lysine

Conditionally indispensable aa's

physiological circumstances can prevent synthesis of an amino acid from its precursor (ie; compromised liver function, inborn errors of metabolism)

Exogenous protein sources:

ingested dietary protein from animal and plant foods

Endogenous protein

-desquamated mucosal cells (50g pro/d)
-digestive enzymes and glycoproteins (17 g pro/d)

Digestion of protein involves denaturation of ______, ______ & _____ by gastric acid, allowing .....

denaturation of the quanternary, tertiary and secondary structures by gastric acid, allowing enzyme access for hydrolysis of the peptide bonds in the primary structure.

Enzymatic "hydrolysis" of peptide bonds begins with _______ in the ______, and involves the addition of ____ molecule of _____.

pepsin in stomach
involves the addition of 1 molecule of water

Enzymes involved in digestion of protein in the stomach:

-Pepsin (Pepsinogen)
[ Pepsinogen --HCl--> Pepsin ]

Enzymes involved in digestion of protein in the sm intestine:

-Trypsin (trypsinogen)
-Chymotrypsin (chymotrypsinogen)
-Carboxypeptidase A & B (procarboxypeptidase A/B)
-Elastase (proelastase)

Enzymes involved in digestion of protein in brush border:

amino, di and tri -peptidases

Intestinal absorption of amino acids is a ________ mechanism - only ____% of amino acids are absorbed as free amino acids.

secondary mechanism

There are specific and overlapping transporters for various AA's; most transporters are ________ dependent.

Na+ dependent

Essential and branched chain AA's are absorbed __________ than non-essential and smaller AA's

absorbed faster

Supplemental amino acids may _______ for absorption, resulting in ________.


Nitrogen retention is ________ from amino acid supplements than from food sources.

nitrogen retention is greater for protein from food sources.

What is the primary form of amino acid absorption?

Absortion of Peptides is the primary mechanism for aa absorption

_____% of amino acids are absorbed as peptides.


Di and tri -peptides are absorbed ________ than amino acids.

absorbed faster

Specific transporters for peptides are:

- H+ co-transport
- H+/Na+ exchange at brush border
- Na+/K+ exchange at basolateral membrane

Absorbed amino acids in the enterocyte are retained for synthesis of:

-Digestive enzymes (brush border)
-Nitrogen-containing compounds
-Other amino acids

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